It started when the money collected at a city-owned parking garage began to drop mysteriously, turning one of Lawrence’s few cash cows into a source of worry. The losses got bad enough — averaging $7,000 per month — that someone called the FBI.

So began yet another corruption investigation in Lawrence, one of Massachusetts’ most beleaguered cities, putting the administration of Mayor William Lantigua in the crosshairs again.

Investigators have zeroed in on Justo Garcia, the Museum Square Garage office manager who is also Lantigua’s campaign photographer and former State House employee, according to someone briefed on the alleged theft. Officials contacted the FBI after noticing a steady decline in monthly pass revenues that could not be explained.

“A cash revenue decrease of that nature is a red flag and highly unusual,” said Michael Sweeney, Lawrence’s former planning director, whose duties included administering the city’s garages and parking lots. “Just like in Vegas, there must always be two people that independently log and verify cash receipts. That appears to be missing here.”

Garcia runs the pass program and was the employee responsible for the money, according to the person briefed on the investigation, who asked not to be identified because the probe is confidential. Using marked bills, the FBI found that cash used to pay for monthly passes did not always end up in the city coffers, according to this person.

Garcia, who in September appeared before a state grand jury investigating Lantigua’s administration, could not be reached for comment. Lantigua also could not be reached for comment.

The garage investigation continues more than three years of controversy that have dogged the city since Lantigua was elected in 2009 on an initial wave of good will as the state’s first Latino mayor. Lantigua’s charisma and inspiring biography — a native of the Dominican Republic who rose to be a state representative and then to lead an American city of 76,000 — were quickly overtaken by a drumbeat of investigations and scandals.

Already, two of Lantigua’s closest allies are awaiting trial on public corruption charges. Former deputy police chief Melix Bonilla, Lantigua’s former campaign manager, and Leonard Degnan, his former chief of staff, were indicted last September on five counts including extortion and conspiracy.

Earlier this year, Lantigua paid a $5,000 fine to settle a lawsuit brought by Attorney General Martha Coakley over his failure to file a required campaign finance report for months. In addition, Lantigua’s girlfriend, city employee Lorenza Ortega, had to repay $500 in home energy assistance in 2011 after it became public that the couple had received public aid despite a combined household income of $145,000.

Despite the near-constant turmoil and two failed attempts by voters to recall him from office, Lantigua is campaigning for reelection to a second four-year term this November. Six candidates are looking to oust the mayor, who has raised little money. Lantigua had only $15,683 in his campaign bank account at the end of 2012, the latest report available.

One of Lantigua’s opponents, Lawrence City Councilor at Large Daniel Rivera, said the negative press generated by Lantigua is “killing” the city and its residents.

“We have all these hard-working families and small business trying to make it through the week,” he said. “They deserve a mayor who supports them and makes headlines that are good about Lawrence, not negative. This stuff is killing them. The hard-working people are collateral damage.

“No one wants to have a 01840 zip code. He makes it hard for us to be the best Lawrence it can be if all that is in the newspaper is the negative stuff going on in the administration,” Rivera said.

Lantigua has acknowledged that he seems to be a magnet for controversy, but he has portrayed himself and his administration as victims of dirty politics. “If it’s not one thing, it’s another and another and another,” he told the Globe last year. “Where am I going to get the money for an attorney every week? . . . All I know is that at the end of the day, I have done nothing wrong.”

At the Museum Square Garage, a rare profit center in a city that needed a state financial bailout a few years ago, Lantigua assigned Garcia to the $19-an-hour garage job in 2010, according to the person briefed on the investigation. Citywide, the number of employees at the city’s garages and parking lots has more than doubled under Lantigua from nine to 22, according to this person.

Officials noticed the decline in revenues last year, the source said. Monthly revenues from the city-owned garage, located across the street from the Lawrence District Court, had dipped from a high of more than $31,000 to around $18,000, the source said.

FBI investigators then purchased monthly passes using marked bills to determine whether the money went to city accounts, this person said.

The investigation into the garage revenues is part of a larger, ongoing corruption probe that has already led to the indictment of two of Lantigua’s closest associates.

Degnan, Lantigua’s former chief of staff, has been accused of using his position to illegally pressure the city’s waste contractor to donate a garbage truck to a remote city in the Dominican Republic.

Degnan “demanded” Allied Waste donate a trash truck to the city in the Dominican Republic, Lantigua’s native country, threatening to void the company’s three-year, $6.4 million contract with the City of Lawrence, the indictments said. An Allied Waste executive complied with his demand “out of fear of having its contract voided,” the indictment said.

Bonilla, Lantigua’s 2009 campaign manager, allegedly falsely transferred ownership of 13 motor vehicles from the Police Department to an auto dealer with ties to Lantigua. In exchange for the 13 seized vehicles, which included a Cadillac, Lexus, and Acura, the city received four Chevrolet Impalas – vehicles worth half as much.

Bonilla was charged with threatening another employee of the Police Department, forcing him to sign over the titles to the vehicles against his will. The employee complied “due to the actions of Melix Bonilla,” the indictment said.

Degnan and Bonilla are both facing potentially lengthy prison sentences if convicted. Degnan also faces charges of solicitation of a bribe with corrupt intent, knowing solicitation of a bribe, unlawful use of official position, and extortion or attempted extortion.

Bonilla also faces charges of fraudulent conversion of city property, unlawful use of official position, conspiracy, extortion or attempted extortion, and trick, scheme, or device to mislead in the procurement of supplies.

The person familiar with the garage investigation said that the suspected wrongdoing may go beyond theft. This person said that Garcia also appears to be doing political work for Lantigua while managing at the garage, writing greeting cards, and other mailings for Lantigua to send to voters on city time.

Under state law, it is illegal to use public buildings and other government resources to do political work.

Maria Sacchetti and Sean P. Murphy of the Globe staff contributed to this report. Andrea Estes can be reached at estes@globe.com.

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